Honors & Awards

  • Research Fellow of JSPS (DC1), Japan Society for the Promotion of Science (JSPS) (2009-2012)
  • JSPS Postdoctoral Fellowship for Overseas Researchers (Standard), Japan Society for the Promotion of Science (JSPS) (2017-2019)

Professional Education

  • Bachelor of Science, University Of Tokyo (2007)
  • Master of Science, University Of Tokyo (2009)
  • Doctor of Philosophy, University Of Tokyo (2012)

Stanford Advisors

Research & Scholarship

Current Research and Scholarly Interests

In my undergraduate and graduate school, my research interests are in the development of bloods cells especially immune cells from hematopoietic stem cells (HSCs). As an undergraduate, I conducted research with Dr. Hitoshi Sakano on elucidating the mechanism of the diversification of the immune receptors in jaw-less animals (more primitive species than fish) such as sea lamprey and hagfish. Sea lamprey and hagfish has different type of immune receptor gene from T-cell receptor (TCR) or Immunoglobulin (Ig), and gene assembly other than V(D)J recombination occurs on the gene for diversifying it. By using immunogenetics, molecular biology, and computational method I uncovered the way for diversifying the immune receptor gene in these species.

I switched my research field to rodents in my former half of Ph.D. course. With Dr. Hiromitsu Nakauchi I focused on generating transplantable HSC from mouse embryonic stem cells (ESCs). I could purify and phenotyped the population which have the capacity for engrafting and repopulating in mouse bone marrow after transplantation. In latter half of Ph.D. course, I combined my knowledge about immunology with HSC induction technique for generating immune cells from human induced pluripotent stem cells (iPSCs). I succeeded to obtain abundant and highly functional antigen-specific T cells from human iPSCs, along with rejuvenating the exhausted state by passing through iPSC-reprogramming and redifferentiation.

For research in postdoctoral fellow, I choose to generate 3D organs from human iPSCs. It is very challenging theme but I?m thinking my experiences, knowledge, and techniques in pluripotent stem cells should bear fruit. I continue the T-cell generation research and I?m planning to translate the T-cell products to clinic.


All Publications

  • Efficient scarless genome editing in human pluripotent stem cells. Nature methods Ikeda, K., Uchida, N., Nishimura, T., White, J., Martin, R. M., Nakauchi, H., Sebastiano, V., Weinberg, K. I., Porteus, M. H. 2018; 15 (12): 1045?47


    Scarless genome editing in human pluripotent stem cells (hPSCs) represents a goal for both precise research applications and clinical translation of hPSC-derived therapies. Here we established a versatile and efficient method that combines CRISPR-Cas9-mediated homologous recombination with positive-negative selection of edited clones to generate scarless genetic changes in hPSCs.

    View details for DOI 10.1038/s41592-018-0212-y

    View details for PubMedID 30504872

  • Functional Analysis of Dendritic Cells Generated from T-iPSCs from CD4+T Cell Clones of Sjogren's Syndrome STEM CELL REPORTS Iizuka-Koga, M., Asashima, H., Ando, M., Lai, C., Mochizuki, S., Nakanishi, M., Nishimura, T., Tsuboi, H., Hirota, T., Takahashi, H., Matsumoto, I., Otsu, M., Sumida, T. 2017; 8 (5): 1155-1163


    Although it is important to clarify the pathogenic functions of Tácells in human samples, their examination is often limited due to difficulty in obtaining sufficient numbers of dendritic cells (DCs), used as antigen-presenting cells, especially in autoimmune diseases. We describe the generation of DCs from induced pluripotent stem cells derived from Tácells (T-iPSCs). We reprogrammed CD4+ Tácell clones from a patient with Sj÷gren's syndrome (SS) into iPSCs, which were differentiated into DCs (T-iPS-DCs). T-iPS-DCs had dendritic cell-like morphology, and expressed CD11c, HLA-DR, CD80, CD86, and also BDCA-3. Compared with monocyte-derived DCs, the capacity for antigen processing was similar, and T-iPS-DCs induced the proliferative response of autoreactive CD4+ Tácells. Moreover, we could evaluate Tácell functions of the patient with SS. In conclusion, we obtained adequate numbers of DCs from T-iPSCs, which could be used to characterize pathogenic Tácells in autoimmune diseases such as SS.

    View details for DOI 10.1016/j.stemcr.2017.04.010

    View details for Web of Science ID 000401129400005

    View details for PubMedID 28494936

  • Human AML-iPSCs Reacquire Leukemic Properties after Differentiation and Model Clonal Variation of Disease. Cell stem cell Chao, M. P., Gentles, A. J., Chatterjee, S., Lan, F., Reinisch, A., Corces, M. R., Xavy, S., Shen, J., Haag, D., Chanda, S., Sinha, R., Morganti, R. M., Nishimura, T., Ameen, M., Wu, H., Wernig, M., Wu, J. C., Majeti, R. 2017; 20 (3): 329-344 e7


    Understanding the relative contributions of genetic and epigenetic abnormalities to acute myeloid leukemia (AML) should assist integrated design of targeted therapies. In this study, we generated induced pluripotent stem cells (iPSCs) from AML patient samples harboring MLL rearrangements and found that they retained leukemic mutations but reset leukemic DNA methylation/gene expression patterns. AML-iPSCs lacked leukemic potential, but when differentiated into hematopoietic cells, they reacquired the ability to give rise to leukemia inávivo and reestablished leukemic DNA methylation/gene expression patterns, including an aberrant MLL signature. Epigenetic reprogramming was therefore not sufficient to eliminate leukemic behavior. This approach also allowed us to study the properties of distinct AML subclones, including differential drug susceptibilities of KRAS mutant and wild-type cells, and predict relapse based on increased cytarabine resistance of a KRAS wild-type subclone. Overall, our findings illustrate the value of AML-iPSCs for investigating the mechanistic basis and clonal properties of human AML.

    View details for DOI 10.1016/j.stem.2016.11.018

    View details for PubMedID 28089908

  • An All-Recombinant Protein-Based Culture System Specifically Identifies Hematopoietic Stem Cell Maintenance Factors. Stem cell reports Ieyasu, A., Ishida, R., Kimura, T., Morita, M., Wilkinson, A. C., Sudo, K., Nishimura, T., Ohehara, J., Tajima, Y., Lai, C., Otsu, M., Nakamura, Y., Ema, H., Nakauchi, H., Yamazaki, S. 2017


    Hematopoietic stem cells (HSCs) are considered one of the most promising therapeutic targets for the treatment of various blood disorders. However, due to difficulties in establishing stable maintenance and expansion of HSCs inávitro, their insufficient supply is a major constraint to transplantation studies. To solve these problems we have developed a fully defined, all-recombinant protein-based culture system. Through this system, we have identified hemopexin (HPX) and interleukin-1? as responsible for HSC maintenance inávitro. Subsequent molecular analysis revealed that HPX reduces intracellular reactive oxygen species levels within cultured HSCs. Furthermore, bone marrow immunostaining and 3D immunohistochemistry revealed that HPX is expressed in non-myelinating Schwann cells, known HSC niche constituents. These results highlight the utility of this fully defined all-recombinant protein-based culture system for reproducible inávitro HSC culture and its potential to contribute to the identification of factors responsible for inávitro maintenance, expansion, and differentiation of stem cell populations.

    View details for DOI 10.1016/j.stemcr.2017.01.015

    View details for PubMedID 28238792

  • Thalidomide induces apoptosis in undifferentiated human induced pluripotent stem cells. In vitro cellular & developmental biology. Animal Tachikawa, S., Nishimura, T., Nakauchi, H., Ohnuma, K. 2017


    Thalidomide, which was formerly available commercially to control the symptoms of morning sickness, is a strong teratogen that causes fetal abnormalities. However, the mechanism of thalidomide teratogenicity is not fully understood; thalidomide toxicity is not apparent in rodents, and the use of human embryos is ethically and technically untenable. In this study, we designed an experimental system featuring human-induced pluripotent stem cells (hiPSCs) to investigate the effects of thalidomide. These cells exhibit the same characteristics as those of epiblasts originating from implanted fertilized ova, which give rise to the fetus. Therefore, theoretically, thalidomide exposure during hiPSC differentiation is equivalent to that in the human fetus. We examined the effects of thalidomide on undifferentiated hiPSCs and early-differentiated hiPSCs cultured in media containing bone morphogenetic protein-4, which correspond, respectively, to epiblast (future fetus) and trophoblast (future extra-embryonic tissue). We found that only the number of undifferentiated cells was reduced. In undifferentiated cells, application of thalidomide increased the number of apoptotic and dead cells at day 2 but not day 4. Application of thalidomide did not affect the cell cycle. Furthermore, immunostaining and flow cytometric analysis revealed that thalidomide exposure had no effect on the expression of specific markers of undifferentiated and early trophectodermal differentiated cells. These results suggest that the effect of thalidomide was successfully detected in our experimental system and that thalidomide eliminated a subpopulation of undifferentiated hiPSCs. This study may help to elucidate the mechanisms underlying thalidomide teratogenicity and reveal potential strategies for safely prescribing this drug to pregnant women.

    View details for DOI 10.1007/s11626-017-0192-8

    View details for PubMedID 28849348

  • Inhibition of Apoptosis Overcomes Stage-Related Compatibility Barriers to Chimera Formation in Mouse Embryos. Cell stem cell Masaki, H., Kato-Itoh, M., Takahashi, Y., Umino, A., Sato, H., Ito, K., Yanagida, A., Nishimura, T., Yamaguchi, T., Hirabayashi, M., Era, T., Loh, K. M., Wu, S. M., Weissman, I. L., Nakauchi, H. 2016; 19 (5): 587-592


    Cell types more advanced in development than embryonic stem cells, such as EpiSCs, fail to contribute to chimeras when injected into pre-implantation-stage blastocysts, apparently because the injected cells undergo apoptosis. Here we show that transient promotion of cell survival through expression of the anti-apoptotic gene BCL2 enables EpiSCs and Sox17(+) endoderm progenitors to integrate into blastocysts and contribute to chimeric embryos. Upon injection into blastocyst, BCL2-expressing EpiSCs contributed to all bodily tissues in chimeric animals while Sox17(+) endoderm progenitors specifically contributed in a region-specific fashion to endodermal tissues. In addition, BCL2 expression enabled rat EpiSCs to contribute to mouse embryonic chimeras, thereby forming interspecies chimeras that could survive to adulthood. Our system therefore provides a method to overcome cellular compatibility issues that typically restrict chimera formation. Application of this type of approach could broaden the use of embryonic chimeras, including region-specific chimeras, for basic developmental biology research and regenerative medicine.

    View details for DOI 10.1016/j.stem.2016.10.013

    View details for PubMedID 27814480

  • A Safeguard System for Induced Pluripotent Stem Cell-Derived Rejuvenated T Cell Therapy STEM CELL REPORTS Ando, M., Nishimura, T., Yamazaki, S., Yamaguchi, T., Kawana-Tachikawa, A., Hayama, T., Nakauchi, Y., Ando, J., Ota, Y., Takahashi, S., Nishimura, K., Ohtaka, M., Nakanishi, M., Miles, J. J., Burrows, S. R., Brenner, M. K., Nakauchi, H. 2015; 5 (4): 597-608


    The discovery of induced pluripotent stem cells (iPSCs) has created promising new avenues for therapies in regenerative medicine. However, the tumorigenic potential of undifferentiated iPSCs is a major safety concern for clinical translation. To address this issue, we demonstrated the efficacy of suicide gene therapy by introducing inducible caspase-9 (iC9) into iPSCs. Activation of iC9 with a specific chemical inducer of dimerization (CID) initiates a caspase cascade that eliminates iPSCs and tumors originated from iPSCs. We introduced this iC9/CID safeguard system into a previously reported iPSC-derived, rejuvenated cytotoxic T lymphocyte (rejCTL) therapy model and confirmed that we can generate rejCTLs from iPSCs expressing high levels of iC9 without disturbing antigen-specific killingáactivity. iC9-expressing rejCTLs exert antitumor effects inávivo. The system efficiently and safely induces apoptosis in these rejCTLs. These results unite to suggest that the iC9/CID safeguard system is a promising tool for future iPSC-mediated approaches to clinical therapy.

    View details for DOI 10.1016/j.stemcr.2015.07.011

    View details for Web of Science ID 000364990900013

    View details for PubMedID 26321144

  • Impaired hematopoietic differentiation of RUNX1-mutated induced pluripotent stem cells derived from FPD/AML patients LEUKEMIA Sakurai, M., Kunimoto, H., Watanabe, N., Fukuchi, Y., Yuasa, S., Yamazaki, S., Nishimura, T., Sadahira, K., Fukuda, K., Okano, H., Nakauchi, H., Morita, Y., Matsumura, I., Kudo, K., Ito, E., Ebihara, Y., Tsuji, K., Harada, Y., Harada, H., Okamoto, S., Nakajima, H. 2014; 28 (12): 2344-2354


    Somatic mutation of RUNX1 is implicated in various hematological malignancies, including myelodysplastic syndrome and acute myeloid leukemia (AML), and previous studies using mouse models disclosed its critical roles in hematopoiesis. However, the role of RUNX1 in human hematopoiesis has never been tested in experimental settings. Familial platelet disorder (FPD)/AML is an autosomal dominant disorder caused by germline mutation of RUNX1, marked by thrombocytopenia and propensity to acute leukemia. To investigate the physiological function of RUNX1 in human hematopoiesis and pathophysiology of FPD/AML, we derived induced pluripotent stem cells (iPSCs) from three distinct FPD/AML pedigrees (FPD-iPSCs) and examined their defects in hematopoietic differentiation. By in vitro differentiation assays, FPD-iPSCs were clearly defective in the emergence of hematopoietic progenitors and differentiation of megakaryocytes, and overexpression of wild-type (WT)-RUNX1 reversed most of these phenotypes. We further demonstrated that overexpression of mutant-RUNX1 in WT-iPSCs did not recapitulate the phenotype of FPD-iPSCs, showing that the mutations were of loss-of-function type. Taken together, this study demonstrated that haploinsufficient RUNX1 allele imposed cell-intrinsic defects on hematopoietic differentiation in human experimental settings and revealed differential impacts of RUNX1 dosage on human and murine megakaryopoiesis. FPD-iPSCs will be a useful tool to investigate mutant RUNX1-mediated molecular processes in hematopoiesis and leukemogenesis.Leukemia advance online publication, 13 May 2014; doi:10.1038/leu.2014.136.

    View details for DOI 10.1038/leu.2014.136

    View details for Web of Science ID 000346177500011

    View details for PubMedID 24732596

  • Generation of Rejuvenated Antigen-Specific T Cells by Reprogramming to Pluripotency and Redifferentiation CELL STEM CELL Nishimura, T., Kaneko, S., Kawana-Tachikawa, A., Tajima, Y., Goto, H., Zhu, D., Nakayama-Hosoya, K., Iriguchi, S., Uemura, Y., Shimizu, T., Takayama, N., Yamada, D., Nishimura, K., Ohtaka, M., Watanabe, N., Takahashi, S., Iwamoto, A., Koseki, H., Nakanishi, M., Eto, K., Nakauchi, H. 2013; 12 (1): 114-126


    Adoptive immunotherapy with functional Tácells is potentially an effective therapeutic strategy for combating many types of cancer and viral infection. However, exhaustion of antigen-specific Tácells represents a major challenge to this type of approach. In an effort to overcome this problem, we reprogrammed clonally expanded antigen-specific CD8(+) Tácells from an HIV-1-infected patient to pluripotency. The Tácell-derived induced pluripotent stem cells were then redifferentiated into CD8(+) Tácells that had a high proliferative capacity and elongated telomeres. These "rejuvenated" cells possessed antigen-specific killing activity and exhibited Tácell receptor gene-rearrangement patterns identical to those of the original Tácell clone from the patient. We also found that this method can be effective for generating specific Tácells for other pathology-associated antigens. Thus, this type of approach may have broad applications in the field of adoptive immunotherapy.

    View details for DOI 10.1016/j.stem.2012.11.002

    View details for Web of Science ID 000313839500015

    View details for PubMedID 23290140

  • Stepwise Development of Hematopoietic Stem Cells from Embryonic Stem Cells PLOS ONE Matsumoto, K., Isagawa, T., Nishimura, T., Ogaeri, T., Eto, K., Miyazaki, S., Miyazaki, J., Aburatani, H., Nakauchi, H., Ema, H. 2009; 4 (3)


    The cellular ontogeny of hematopoietic stem cells (HSCs) remains poorly understood because their isolation from and their identification in early developing small embryos are difficult. We attempted to dissect early developmental stages of HSCs using an in vitro mouse embryonic stem cell (ESC) differentiation system combined with inducible HOXB4 expression. Here we report the identification of pre-HSCs and an embryonic type of HSCs (embryonic HSCs) as intermediate cells between ESCs and HSCs. Both pre-HSCs and embryonic HSCs were isolated by their c-Kit(+)CD41(+)CD45(-) phenotype. Pre-HSCs did not engraft in irradiated adult mice. After co-culture with OP9 stromal cells and conditional expression of HOXB4, pre-HSCs gave rise to embryonic HSCs capable of engraftment and long-term reconstitution in irradiated adult mice. Blast colony assays revealed that most hemangioblast activity was detected apart from the pre-HSC population, implying the early divergence of pre-HSCs from hemangioblasts. Gene expression profiling suggests that a particular set of transcripts closely associated with adult HSCs is involved in the transition of pre-HSC to embryonic HSCs. We propose an HSC developmental model in which pre-HSCs and embryonic HSCs sequentially give rise to adult types of HSCs in a stepwise manner.

    View details for DOI 10.1371/journal.pone.0004820

    View details for Web of Science ID 000265496400002

    View details for PubMedID 19287487

  • Antigen-receptor genes of the agnathan lamprey are assembled by a process involving copy choice NATURE IMMUNOLOGY Nagawa, F., Kishishita, N., Shimizu, K., Hirose, S., Miyoshi, M., Nezu, J., Nishimura, T., Nishizumi, H., Takahashi, Y., Hashimoto, S., Takeuchi, M., Miyajima, A., Takemori, T., Otsuka, A. J., Sakano, H. 2007; 8 (2): 206-213


    Jawless vertebrates have acquired immunity but do not have immunoglobulin-type antigen receptors. Variable lymphocyte receptors (VLRs) have been identified in lamprey that consist of multiple leucine-rich repeat (LRR) modules. An active VLR gene is generated by the assembly of a series of variable gene segments, including many that encode LRRs. Stepwise assembly of the gene segments seems to occur by replacement of the intervening DNA between the 5' and 3' constant-region genes. Here we report that lamprey (Lethenteron japonicum) assemble their VLR genes by a process involving 'copy choice'. Regions of short homology seemed to prime copying of donor LRR-encoding sequences into the recipient gene. Those LRR-encoding germline sequences were abundant and shared extensive sequence homologies. Such genomic organization permits initiation of copying anywhere in an LRR-encoding module for the generation of various hybrid LRRs. Thus, a vast repertoire of recombinant VLR genes could be generated not only by copying of various LRR segments in diverse combinations but also by the use of multiple sites in an LRR gene segment for priming.

    View details for DOI 10.1038/ni1419

    View details for Web of Science ID 000243597600019

    View details for PubMedID 17187071

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